genome.fa.s4.2.7.7.80.10.50.1000.97.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  97  of  198  ( 23681 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31063685--31063717	12	2.8	12	90	0	57	24	33	9	33	1.87
31072460--31072490	8	3.9	8	95	0	53	9	9	25	54	1.63
31072764--31072798	11	3.2	11	100	0	70	74	8	0	17	1.06
31074456--31074847	50	7.7	50	85	3	439	23	28	20	27	1.99
31075469--31075535	32	2.1	31	83	8	82	41	11	7	38	1.70
31075480--31075545	32	2.1	32	97	0	123	37	13	9	39	1.77
31077564--31078003	219	2.0	219	95	0	799	26	26	15	31	1.95
31085882--31085941	25	2.4	23	81	13	66	35	1	1	61	1.16
31087636--31087711	28	2.8	28	79	2	82	21	13	25	40	1.89
31092099--31092145	10	4.5	10	84	10	58	36	0	2	61	1.08
31092101--31092145	12	4.2	11	83	16	58	33	0	2	64	1.06
31099698--31099740	18	2.4	17	77	11	50	60	4	9	25	1.47
31101501--31101554	25	2.2	25	82	0	63	24	24	20	31	1.98
31104277--31104382	20	5.3	20	68	7	74	44	16	25	14	1.85
31104336--31104390	19	2.8	21	81	13	80	49	20	20	10	1.78
31107034--31107058	13	1.9	13	100	0	50	32	4	24	40	1.73
31108103--31108261	43	3.7	43	80	7	146	23	17	27	31	1.97
31116152--31116229	39	2.0	39	87	0	111	44	23	3	28	1.70
31116760--31116862	30	3.5	29	83	10	120	26	25	28	20	1.99
31116987--31117050	26	2.5	26	86	0	92	45	21	15	17	1.85
31117245--31117492	27	9.2	27	79	3	205	22	16	18	43	1.88
31119458--31119578	30	4.1	29	77	5	109	28	22	24	24	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31119688--31119787	26	3.8	26	81	5	121	42	24	20	14	1.88
31119958--31120200	27	9.0	27	84	6	271	21	18	17	42	1.89
31139076--31139360	27	10.6	27	87	0	381	41	21	17	18	1.90
31152379--31152414	17	2.1	17	94	0	63	33	19	8	38	1.82
31157260--31157318	25	2.4	25	88	8	93	59	22	0	18	1.38
31160161--31160557	147	2.6	148	85	6	523	43	4	10	41	1.60
31162620--31162659	20	2.0	21	90	5	64	27	0	10	62	1.27
31164610--31164665	29	1.9	29	85	0	76	48	17	23	10	1.79
31165549--31165586	19	2.0	20	89	5	60	55	5	5	34	1.45
31169427--31169469	20	2.1	21	87	8	63	60	2	4	32	1.30
31170670--31170718	20	2.5	20	75	15	57	14	22	6	57	1.59
31170921--31171162	50	4.7	50	81	4	245	23	28	21	26	1.99
31192519--31192772	136	1.9	136	83	3	332	20	20	27	31	1.97
31196169--31196209	21	2.0	21	85	0	55	7	46	2	43	1.44
31197420--31197467	22	2.1	22	81	11	53	41	0	16	41	1.48
31214562--31214620	25	2.4	25	97	0	109	28	10	18	42	1.83
31214825--31214886	32	1.9	32	96	0	115	43	11	6	38	1.66
31215002--31215182	63	2.9	64	89	4	262	50	7	9	32	1.63
31216714--31216817	49	2.1	49	87	3	147	30	8	11	49	1.69
31218491--31218627	44	3.1	44	95	2	238	36	31	4	27	1.77
31219159--31219398	41	6.0	39	76	8	159	35	27	21	15	1.94
31219185--31219374	38	4.9	38	75	8	143	36	25	21	16	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31225964--31226004	21	2.0	21	90	0	64	46	19	2	31	1.63
31226427--31226776	41	8.8	41	82	3	306	36	27	19	17	1.94
31226553--31226789	38	6.1	38	83	3	224	35	29	19	15	1.92
31227784--31227823	14	2.9	14	84	0	53	32	7	17	42	1.77
31233587--31233643	30	1.9	30	88	0	87	42	22	14	21	1.88
31239772--31239811	20	2.0	20	90	0	62	40	22	27	10	1.86
31242659--31242693	14	2.6	14	90	4	54	42	2	2	51	1.31
31246607--31246638	16	2.0	16	93	0	55	46	18	6	28	1.73
31248590--31248634	19	2.3	20	92	3	74	40	6	4	48	1.49
31266329--31266796	259	1.8	255	84	5	645	33	14	7	44	1.73
31272416--31272452	14	2.6	14	86	0	56	43	2	35	18	1.65
31273409--31273468	30	2.0	31	86	3	86	40	0	40	20	1.52
31274043--31274096	26	2.1	26	82	6	65	33	11	24	31	1.90
31274670--31274983	94	3.4	94	78	3	285	28	15	19	36	1.92
31277308--31277345	19	2.0	19	89	0	58	36	5	15	42	1.70
31277651--31277677	2	13.5	2	100	0	54	48	0	0	51	1.00
31280039--31280087	23	2.1	23	92	0	80	26	8	22	42	1.81
31296093--31296158	33	2.0	33	100	0	132	45	9	12	33	1.73
31296745--31296781	14	2.6	15	83	12	51	2	35	0	62	1.10
31298478--31298526	18	2.6	19	93	6	82	48	0	28	22	1.50
31305893--31305933	21	2.0	21	100	0	82	24	19	9	46	1.80
31305928--31306072	30	4.8	30	73	6	96	26	23	14	35	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31305947--31306071	60	2.1	60	81	3	144	25	24	12	37	1.91
31306061--31306128	29	2.3	29	87	2	100	14	27	14	42	1.85
31306120--31306194	31	2.5	31	88	2	107	25	25	10	38	1.88
31312720--31312919	51	4.0	50	75	10	192	31	27	16	25	1.96
31328726--31328750	12	2.1	12	100	0	50	0	24	0	76	0.80
31330445--31330601	56	2.7	60	83	13	193	40	1	1	56	1.19
31330519--31330610	26	3.4	26	75	11	94	42	2	0	55	1.12
31333724--31333855	70	1.9	67	83	4	165	40	14	13	31	1.85
31336318--31336382	19	3.4	18	81	12	69	26	3	4	66	1.26
31336758--31336825	26	2.5	26	81	11	84	30	1	0	67	0.99
31340854--31340903	3	16.7	3	95	0	91	70	0	30	0	0.88
31346069--31346110	21	2.0	21	86	13	59	4	16	2	76	1.07
31346129--31346156	13	2.2	13	100	0	56	21	7	0	71	1.09
31346310--31346369	20	3.2	19	76	19	63	26	1	5	66	1.21
31348805--31348945	29	4.8	29	78	4	113	36	14	26	22	1.92
31352481--31352664	57	3.1	57	62	22	133	23	11	29	35	1.90
31352420--31352668	122	2.0	123	99	0	491	22	10	28	37	1.88
31363258--31363356	25	4.0	25	78	1	101	31	15	28	25	1.95
31363454--31363513	26	2.3	26	82	0	75	36	21	21	20	1.95
31372083--31372137	27	2.0	27	82	13	67	50	1	1	45	1.22
31374412--31374593	51	3.6	48	79	10	204	24	16	27	31	1.96
31374412--31374598	101	1.8	101	87	5	279	24	16	27	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31374415--31374632	101	2.1	101	83	5	262	26	15	26	31	1.95
31387337--31387423	41	2.1	41	82	4	104	35	27	21	14	1.93
31387433--31387609	38	4.7	38	81	2	203	30	28	23	16	1.97
31387412--31387609	76	2.6	76	84	4	265	31	29	22	16	1.96
31394310--31394583	27	10.1	27	84	1	343	40	22	16	20	1.91
31394749--31394855	26	4.1	26	86	4	126	20	16	23	39	1.92
31406248--31406494	50	4.8	50	79	4	219	23	27	21	27	1.99
31420580--31420669	33	2.8	33	90	6	123	35	20	17	26	1.95
31420601--31420669	33	2.1	33	100	0	138	33	21	17	27	1.96
31421889--31421921	14	2.4	14	100	0	66	21	18	30	30	1.97
31421924--31422083	45	3.6	45	88	3	241	21	14	29	34	1.93
31435275--31435303	12	2.3	13	94	5	51	20	6	6	65	1.40
31444757--31444934	54	3.3	54	84	2	223	41	14	13	30	1.85
31444828--31444916	19	4.8	19	68	18	71	44	12	15	26	1.82
31449203--31449339	54	2.5	54	87	4	195	41	13	11	32	1.81
31449268--31449306	19	2.1	19	95	0	69	48	12	10	28	1.74
31449294--31449360	35	1.9	35	90	0	107	38	13	10	37	1.79
31452021--31452045	3	8.3	3	100	0	50	0	32	0	68	0.90
31452833--31452888	25	2.2	25	87	6	78	58	1	1	37	1.19
31453592--31453625	16	2.2	15	89	5	50	55	0	0	44	0.99
31463856--31463916	27	2.3	26	83	5	70	45	24	13	16	1.83
31465465--31465700	50	4.7	50	86	3	321	29	25	16	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31469978--31470028	26	1.9	27	88	4	77	49	13	9	27	1.74
31471484--31471512	11	2.7	11	94	5	51	58	0	34	6	1.25
31475620--31475658	5	7.8	5	100	0	78	38	0	0	61	0.96
31476047--31476113	28	2.3	30	76	7	75	43	1	7	47	1.40
31476049--31476103	28	1.9	29	85	3	76	47	1	9	41	1.46
31478423--31478483	29	2.1	29	96	0	113	59	13	13	14	1.63
31483034--31483124	29	3.1	29	76	9	87	23	14	21	40	1.90
31486041--31486123	27	3.0	27	77	10	78	33	14	21	30	1.93
31489561--31489606	19	2.3	20	85	7	58	26	4	2	67	1.21
31489598--31489717	59	2.0	62	82	8	149	40	6	15	36	1.74

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198